# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 17:47:16 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 6-deoxy-L-psicose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)[C@H](O)[C@H](O)C(=O)CO
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 PUD  PUD  '6-deoxy-L-psicose        '  ligand  23  11  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PUD
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 PUD  C4   C  CH1   0  -0.008   0.8834  -0.4339   0.3895
 PUD  C2   C  C     0   0.359  -1.5241   0.1910   0.2466
 PUD  C6   C  CH3   0  -0.685   3.2845  -1.1934   0.5296
 PUD  C5   C  CH1   0   0.010   2.2437  -0.4866  -0.3274
 PUD  C1   C  CH2   0  -0.254  -2.4062  -0.6132  -0.6602
 PUD  O1   O  OH1   0  -0.657  -3.6129  -0.9019  -0.0259
 PUD  O2   O  O     0  -0.394  -1.8857   0.5981   1.3245
 PUD  C3   C  CH1   0  -0.099  -0.1259   0.5313  -0.2695
 PUD  O3   O  OH1   0  -0.652   0.1667   1.8737   0.0109
 PUD  O4   O  OH1   0  -0.661   0.3441  -1.7318   0.5099
 PUD  O5   O  OH1   0  -0.658   2.6915   0.7767  -0.7575
 PUD  H1   H  HCH1  0   0.237   1.0291  -0.0822   1.4192
 PUD  H2   H  HCH3  0   0.230   2.9438  -2.1822   0.8358
 PUD  H3   H  HCH3  0   0.239   4.2177  -1.3162  -0.0205
 PUD  H4   H  HCH3  0   0.226   3.4963  -0.6201   1.4356
 PUD  H5   H  HCH1  0   0.225   2.0972  -1.0609  -1.2513
 PUD  H6   H  HCH2  0   0.245  -2.5305  -0.0191  -1.5792
 PUD  H7   H  HCH2  0   0.233  -1.8516  -1.5104  -0.9675
 PUD  H8   H  HOH1  0   0.464  -4.1745  -1.3657  -0.6535
 PUD  H9   H  HCH1  0   0.261  -0.0996   0.4132  -1.3589
 PUD  H10  H  HOH1  0   0.445  -0.0635   2.0426   0.9328
 PUD  H11  H  HOH1  0   0.453   0.3991  -2.1798  -0.3418
 PUD  H12  H  HOH1  0   0.441   2.7166   1.3725  -0.0016

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 PUD  O2  C2   double  1.208  0.020  1.208
 PUD  O3  C3   single  1.402  0.020  1.402
 PUD  C2  C1   single  1.499  0.020  1.499
 PUD  C2  C3   single  1.529  0.020  1.529
 PUD  O1  C1   single  1.394  0.020  1.394
 PUD  C3  C4   single  1.544  0.020  1.544
 PUD  C4  O4   single  1.411  0.020  1.411
 PUD  C4  C5   single  1.539  0.020  1.539
 PUD  O5  C5   single  1.408  0.020  1.408
 PUD  C5  C6   single  1.522  0.020  1.522
 PUD  C4  H1   single  0.970  0.020  1.090
 PUD  C6  H2   single  0.970  0.020  1.090
 PUD  C6  H3   single  0.970  0.020  1.090
 PUD  C6  H4   single  0.970  0.020  1.090
 PUD  C5  H5   single  0.970  0.020  1.090
 PUD  C1  H6   single  0.970  0.020  1.090
 PUD  C1  H7   single  0.970  0.020  1.090
 PUD  O1  H8   single  0.850  0.020  0.980
 PUD  C3  H9   single  0.970  0.020  1.090
 PUD  O3  H10  single  0.850  0.020  0.980
 PUD  O4  H11  single  0.850  0.020  0.980
 PUD  O5  H12  single  0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 PUD  H1   C4  O4  105.39  3.000
 PUD  H1   C4  C3  106.67  3.000
 PUD  O4   C4  C3  111.20  3.000
 PUD  H1   C4  C5  109.31  3.000
 PUD  O4   C4  C5  110.26  3.000
 PUD  C3   C4  C5  113.60  3.000
 PUD  C3   C2  O2  120.01  3.000
 PUD  C3   C2  C1  116.96  3.000
 PUD  O2   C2  C1  123.00  3.000
 PUD  H4   C6  H3  108.15  3.000
 PUD  H4   C6  H2  107.68  3.000
 PUD  H3   C6  H2  107.89  3.000
 PUD  H4   C6  C5  110.83  3.000
 PUD  H3   C6  C5  110.70  3.000
 PUD  H2   C6  C5  111.45  3.000
 PUD  H5   C5  O5  104.77  3.000
 PUD  H5   C5  C6  108.79  3.000
 PUD  O5   C5  C6  111.79  3.000
 PUD  H5   C5  C4  106.99  3.000
 PUD  C6   C5  C4  110.98  3.000
 PUD  O5   C5  C4  113.14  3.000
 PUD  H7   C1  H6  105.31  3.000
 PUD  H7   C1  O1  113.28  3.000
 PUD  H6   C1  O1  113.20  3.000
 PUD  H7   C1  C2  108.08  3.000
 PUD  H6   C1  C2  106.37  3.000
 PUD  O1   C1  C2  110.20  3.000
 PUD  H8   O1  C1  107.98  3.000
 PUD  H9   C3  O3  107.27  3.000
 PUD  H9   C3  C2  109.48  3.000
 PUD  O3   C3  C2  109.66  3.000
 PUD  H9   C3  C4  109.95  3.000
 PUD  C2   C3  C4  108.34  3.000
 PUD  O3   C3  C4  112.13  3.000
 PUD  H10  O3  C3  107.99  3.000
 PUD  H11  O4  C4  109.29  3.000
 PUD  H12  O5  C5  108.89  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 PUD  Var_01  O2  C2  C1  O1  -5.22  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 PUD  chir_01  C4  C3  O4  C5  negativ
 PUD  chir_02  C5  O5  C4  C6  positiv
 PUD  chir_03  C3  O3  C4  C2  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 PUD  plan-1  C2  0.020
 PUD  plan-1  C1  0.020
 PUD  plan-1  O2  0.020
 PUD  plan-1  C3  0.020

